Asylum of the Daleks~ The Doctor, Amy, and Rory are kidnapped by the Daleks, who explain that a planet they use as an asylum for mad Daleks must be destroyed, but to do that its force-field must be disabled. The field has already been ruptured due to the crash-landing of a precocious young woman, Oswin Oswald (Jenna-Louise Coleman) one year previously. The Daleks provide the three with bracelets to protect them against the planet's defense system, which will convert any visitors into Dalek puppets. Although they are guided by Oswin, who has hacked into the planet's systems, the converted remains of Oswin's crew steal Amy's bracelet. The Doctor goes to find Oswin, as she claims to be able to disable the planet's force-field, and Oswin hacks into the Dalek psychic linkand erases all memory of the Doctor from the Daleks who had started to advance on him. The Doctor discovers that Oswin has herself been fully converted into a Dalek, yet she still believes herself to be human. She ultimately realises the truth of her situation, but lowers the force-field and the Doctor, Amy, and Rory escape via teleporter before the planet is destroyed by Daleks. The Doctor returns to the Dalek Parliament to find they have no memory of him due to Oswin's interference.
Dinosaurs on a Spaceship~ The Doctor attempts to prevent the destruction of an unmanned spaceship with a cargo of dinosaurs alongside Rory's father, Brian (Mark Williams), Queen Nefertiti (Riann Steele), and big-game hunter John Riddell (Rupert Graves). The Doctor and his companions discover that the ship is a Silurian ark designed to carry the reptilian humanoids to a new planet along with flora and fauna from their time period. The Doctor, Rory, and Brian are escorted by two robots to a human called Solomon who was injured in a raptor attack. Solomon, who had boarded the spaceship and killed its Silurian inhabitants in order to sell the dinosaurs on board, threatens the Doctor into repairing his legs and into giving him Queen Nefertiti after seeing her value. Missiles are fired from Earth to stop the ship from crashing into it. The Doctor disables Solomon's robots and rescues Nefertiti before he tricks the missiles into targeting Solomon's ship and detaching it from the Silurian ark, whereupon the missiles destroy his ship, killing Solomon. Meanwhile, Rory and Brian pilot the ark away from the Earth. With this done, Brian has gained a sense of adventure; he now travels the world. The Doctor, in the meantime, has taken the dinosaurs to their new home, Siluria.
A Town called Mercy~ The TARDIS accidentally lands in a town in the American West c. 1870 where the TARDIS crew discovers an alien, Jex, acting as the town's doctor, who is being sought by the Gunslinger, a cyborg. The Doctor discovers Jex was a scientist who experimented on volunteers to create cyborgs to fight in a war on his home planet; the Gunslinger is seeking revenge for what was done to him. To prevent the deaths of the townsfolk, he then offers Jex to the Gunslinger, but Amy talks him out of this. However, while the Doctor still believes Jex must answer for his crimes, when the town marshal sacrifices himself to protect Jex from a blast fired by the Gunslinger, he has a change of heart. Seeing that the Gunslinger can track Jex by his facial mark, the Doctor creates a distraction by having the townsfolk paint the mark on their faces and run about; Jex can reach his spaceship and escape with this occurring. However, when it would appear the Gunslinger would follow Jex and involve others in his vendetta again, Jex commits suicide by blowing up this spaceship. Without a purpose now that his vendetta has been completed and because he is nothing more than a weapon of war, the Gunslinger prepares to self-destruct. However, the Doctor talks him out of it and makes him the new marshal of Mercy.
The Power of Three~ Amy and Rory begin to wonder whether they should choose between normal life and "Doctor Life"; when they go away with him they become a part of his life, but the Doctor hasn't been around long enough to be a part of theirs. This all changes when several black cubes appear around the world. Because they are inactive and pose no threat the Doctor begins going insane with boredom; he goes away for a while leaving UNIT in charge of keeping an eye on the cubes. An entire year goes by and the cubes suddenly begin activating random features before stopping the hearts of one third of humanity. The Doctor eventually tracks the cubes to the Shakri, the self-proclaimed "pest-controllers" of the universe; they are eliminating humanity before they can colonise in space, believing them to be an infestation. The Doctor reverses the electric pulse used to stop people's hearts and brings back those who were killed by it, blowing up the Shakri ship. At Brian's urging the Doctor takes Amy and Rory back as full-time companions.
The Angels take Manhatten~ The Doctor takes Amy and Rory to Central Park. While the Doctor is reading Amy a novel about a character called Melody Malone, Rory is taken by a Weeping Angel on his way back from getting coffee. In 1938 New York City, Rory meets River Song, posing as a private investigator and, as the Doctor discovers, the author of his Melody Malone novel. The Doctor and Amy use the novel to break their way into a time-locked 1938 and find Rory, while he and River investigate the Angels' takeover of Manhattan. At the Winter Quay hotel, they find an aged Rory on his deathbed, confirming Rory's fate. The Angels created the hotel in order to keep their victims and maintain a constant source of potential energy on which to feed. To escape his fate, Rory and Amy jump off the top of the building to their deaths, creating a paradox that erases the Angels and their hotel. Waking up in a graveyard with the TARDIS, all seems well until Rory is transported by a surviving Angel. Rescuing him with another paradox would rip New York City apart. As the Doctor begs Amy to come back into the TARDIS, she bids him a tearful farewell and allows the Angel send her back to Rory, creating a fixed point in time. Later, the devastated Doctor reads an afterword by Amy in the novel, telling him all is well and asking him not to be alone, as well as requesting he visit young Amelia Pond as she waits for him in the garden.
The Snowmen~ After the loss of Amy and Rory, the Doctor, depressed, hides himself on top of a cloud in Victorian England's London, vowing never to save the world again. Meanwhile, the "Great Intelligence", a form of "memory snow" which can mirror the thoughts of anything around it, hatches a plot to create an army of ice people. While Strax drives the reluctant Doctor around, they both run into Clara, a barmaid. The Doctor refuses to investigate the snowmen and returns to semi-seclusion in the TARDIS, which is parked in a cloud above London, accessible from ground level via a staircase. By following the Doctor, Clara finds the TARDIS, but leaves, without talking to the Doctor. However, Clara soon returns to her regular job as a governess and learns of an imminent danger to her wards and possibly all of humanity. She turns to the Doctor for help and, motivated through Clara's charm and an interesting set of coincidences, the Doctor takes action. Together with Madame Vastra, Jenny Flint, and Strax, the Doctor and Clara are able to defeat the Great Intelligence and its human servant, Doctor Simeon, using ingenuity and the pure energy of a family crying on Christmas Eve. In the process, the Doctor regains his enthusiasm for adventure and heroism, deciding to take Clara on as his companion. However, before the enemies are defeated Clara is thrown off the edge of a cloud and falls to her death, though the Doctor was sure she would survive. At the end of the episode, the Doctor discovers Clara's full name – Clara Oswin Oswald – and comes to the realization that Clara is the same person as Oswin Oswald from the episode "Asylum of the Daleks". He concludes that she is more than likely still alive in some other place and time and leaves in the newly-redesigned TARDIS to find her.The doctor then visits the same graveyard where her 19th century counterpart is buried.